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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Related Experiment Video

Updated: Nov 5, 2025

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
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The SARS-CoV-2 RNA interactome.

Sungyul Lee1, Young-Suk Lee2, Yeon Choi1

  • 1Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.

Molecular Cell
|May 14, 2021
PubMed
Summary
This summary is machine-generated.

This study identifies 109 host RNA-binding proteins (RBPs) interacting with SARS-CoV-2 RNA, revealing 17 antiviral and 8 proviral RBPs crucial for viral replication and host evasion. These findings offer new therapeutic targets.

Keywords:
COVID-19HCoV-OC43LARP1RNARNA interactome captureRNA-binding proteinsSARS-CoV-2coronavirusmass spectrometryvirus

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Area of Science:

  • Virology
  • Molecular Biology
  • Host-Pathogen Interactions

Background:

  • SARS-CoV-2 utilizes host RNA-binding proteins (RBPs) for replication and evades antiviral RBPs.
  • Understanding the SARS-CoV-2 RNA interactome is critical for deciphering viral pathogenesis.

Purpose of the Study:

  • To comprehensively identify host factors that bind SARS-CoV-2 RNA.
  • To delineate the roles of specific RBPs in regulating coronavirus replication and host antiviral responses.

Main Methods:

  • Development of a robust ribonucleoprotein (RNP) capture protocol.
  • Application of RNP capture to SARS-CoV-2 and HCoV-OC43.
  • Transcriptome analyses and knockdown experiments to assess RBP function.

Main Results:

  • Identified 109 host factors directly binding SARS-CoV-2 RNAs.
  • Discovered conserved interactions between coronavirus RNAs and host proteins across different coronaviruses.
  • Delineated 17 antiviral RBPs (e.g., ZC3HAV1, TRIM25) and 8 proviral RBPs (e.g., EIF3D, CSDE1).
  • Identified LARP1 as an antiviral host factor interacting with SARS-CoV-2 RNA.

Conclusions:

  • This study provides a comprehensive catalog of RBPs involved in coronavirus replication.
  • The identified RBPs regulate multiple steps of the mRNA life cycle, impacting viral pathogenesis.
  • The findings open new avenues for developing therapeutic interventions targeting host-virus interactions.